The Fight between the Original pokemon and the Clones. (The second part that made me cry is in this one but I'll show it by itself anyway.)

When Ash sacrificed himself to stop Mew qnd Mew Two's battle and Pikachu trying to bring Ash back. Followed by the  pokemons tears bringing him back.

Just the way they were crying almost made me cry too. ;3

And those are the two Saddest Parts of that movie that made me cry.